Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:00:17 -0400 (Tue, 09 Apr 2019).
Package 1037/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
MSnbase 2.9.3 Laurent Gatto
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: MSnbase |
Version: 2.9.3 |
Command: rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh MSnbase_2.9.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R MSnbase.buildbin-libdir |
StartedAt: 2019-04-09 07:24:48 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 07:26:19 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 90.6 seconds |
RetCode: 0 |
Status: OK |
PackageFile: MSnbase_2.9.3.tgz |
PackageFileSize: 9.117 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh MSnbase_2.9.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R MSnbase.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=MSnbase.buildbin-libdir MSnbase_2.9.3.tar.gz' >>>>>>> * installing *source* package ‘MSnbase’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Spectrum1_class.c -o Spectrum1_class.o Spectrum1_class.c:8:13: warning: unused function '_new_Spectrum1' [-Wunused-function] static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt, ^ 1 warning generated. clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Spectrum2_class.c -o Spectrum2_class.o Spectrum2_class.c:9:13: warning: unused function '_new_Spectrum2' [-Wunused-function] static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt, ^ 1 warning generated. clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c utils.c -o utils.o utils.c:92:15: warning: unused variable 'ret' [-Wunused-variable] int i1, i2, ret; ^ utils.c:107:15: warning: unused variable 'ret' [-Wunused-variable] int i1, i2, ret; ^ utils.c:123:18: warning: unused variable 'ret' [-Wunused-variable] double d1, d2, ret; ^ utils.c:133:18: warning: unused variable 'ret' [-Wunused-variable] double d1, d2, ret; ^ utils.c:121:12: warning: unused function 'compar_double_asc_order' [-Wunused-function] static int compar_double_asc_order(const void *p1, const void *p2) ^ utils.c:131:12: warning: unused function 'compar_double_desc_order' [-Wunused-function] static int compar_double_desc_order(const void *p1, const void *p2) ^ 6 warnings generated. clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.9-bioc/meat/MSnbase.buildbin-libdir/00LOCK-MSnbase/00new/MSnbase/libs ** R ** data *** moving datasets to lazyload DB Registered S3 methods overwritten by 'ggplot2': method from [.quosures rlang c.quosures rlang print.quosures rlang Creating a new generic function for ‘smooth’ in package ‘MSnbase’ Creating a new generic function for ‘trimws’ in package ‘MSnbase’ in method for ‘coerce’ with signature ‘"MSnSet","SummarizedExperiment"’: no definition for class “SummarizedExperiment” in method for ‘coerce’ with signature ‘"SummarizedExperiment","MSnSet"’: no definition for class “SummarizedExperiment” in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra” ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘smooth’ in package ‘MSnbase’ Creating a new generic function for ‘trimws’ in package ‘MSnbase’ in method for ‘coerce’ with signature ‘"MSnSet","SummarizedExperiment"’: no definition for class “SummarizedExperiment” in method for ‘coerce’ with signature ‘"SummarizedExperiment","MSnSet"’: no definition for class “SummarizedExperiment” in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra” ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MSnbase) >>>>>>> >>>>>>> FIXING LINKS FOR MSnbase.buildbin-libdir/MSnbase/libs//MSnbase.so >>>>>>> install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "MSnbase.buildbin-libdir/MSnbase/libs//MSnbase.so" install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "MSnbase.buildbin-libdir/MSnbase/libs//MSnbase.so" install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "MSnbase.buildbin-libdir/MSnbase/libs//MSnbase.so" install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "MSnbase.buildbin-libdir/MSnbase/libs//MSnbase.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "MSnbase.buildbin-libdir/MSnbase/libs//MSnbase.so"